3H2L

Crystal structure of HCV NS5B polymerase in complex with a novel bicyclic dihydro-pyridinone inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of tricyclic 5,6-dihydro-1H-pyridin-2-ones as novel, potent, and orally bioavailable inhibitors of HCV NS5B polymerase.

Ruebsam, F.Murphy, D.E.Tran, C.V.Li, L.S.Zhao, J.Dragovich, P.S.McGuire, H.M.Xiang, A.X.Sun, Z.Ayida, B.K.Blazel, J.K.Kim, S.H.Zhou, Y.Han, Q.Kissinger, C.R.Webber, S.E.Showalter, R.E.Shah, A.M.Tsan, M.Patel, R.A.Thompson, P.A.Lebrun, L.A.Hou, H.J.Kamran, R.Sergeeva, M.V.Bartkowski, D.M.Nolan, T.G.Norris, D.A.Khandurina, J.Brooks, J.Okamoto, E.Kirkovsky, L.

(2009) Bioorg.Med.Chem.Lett. 19: 6404-6412

  • DOI: 10.1016/j.bmcl.2009.09.045

  • PubMed Abstract: 
  • A novel series of non-nucleoside small molecules containing a tricyclic dihydropyridinone structural motif was identified as potent HCV NS5B polymerase inhibitors. Driven by structure-based design and building on our previous efforts in related serie ...

    A novel series of non-nucleoside small molecules containing a tricyclic dihydropyridinone structural motif was identified as potent HCV NS5B polymerase inhibitors. Driven by structure-based design and building on our previous efforts in related series of molecules, we undertook extensive SAR studies, in which we identified a number of metabolically stable and very potent compounds in genotype 1a and 1b replicon assays. This work culminated in the discovery of several inhibitors, which combined potent in vitro antiviral activity against both 1a and 1b genotypes, metabolic stability, good oral bioavailability, and high C(12) (PO)/EC(50) ratios.


    Organizational Affiliation

    Department of Medicinal Chemistry, Anadys Pharmaceuticals, Inc., 5871 Oberlin Drive, Suite 200, San Diego, CA 92121, USA. fruebsam@anadyspharma.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NS5B polymerase
A, B
578Hepatitis C virus genotype 1b (isolate BK)Mutation(s): 1 
Find proteins for P26663 (Hepatitis C virus genotype 1b (isolate BK))
Go to UniProtKB:  P26663
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YAK
Query on YAK

Download SDF File 
Download CCD File 
A, B
N-{3-[(4aR,7aS)-1-(4-fluorobenzyl)-4-hydroxy-2-oxo-2,4a,5,6,7,7a-hexahydro-1H-cyclopenta[b]pyridin-3-yl]-1,1-dioxido-2H-1,2,4-benzothiadiazin-7-yl}methanesulfonamide
C23 H23 F N4 O6 S2
PAEBVIJMNXTTAT-AEFFLSMTSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.548α = 90.00
b = 106.908β = 90.00
c = 126.575γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
EPMRphasing
HKL-2000data collection
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance